MolNFT v1 · #143239 · protein

39S Fab bound to HER2 ecd

6ATT · Receptor tyrosine-protein kinase erbb-2: “39S Fab bound to HER2 ecd”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.66). MolNFT v1 #143239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ATT
Type: protein
Length: 1,011 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Receptor tyrosine-protein kinase erbb-2; Antibody 39S Fab heavy chain; Antibody 39S Fab…
EC: 2.7.10.1
UniProt: P04626
Ligands: NAG
Pockets: 11 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1)	protein	567	11% helix, 25% strand	P04626
H	Antibody 39S Fab heavy chain	protein	224	4% helix, 53% strand	—
L	Antibody 39S Fab light chain	protein	220	5% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	511	0.66	0.77	57	empty
2	559	0.61	0.74	59	empty
3	152	0.55	0.81	22	empty
4	152	0.55	0.81	21	empty
5	63	0.49	0.85	18	empty

Interfaces

3 interfaces between chains.

H–L · 1997 Å² buried · 16 hydrogen bonds · protein-protein
A–L · 353 Å² buried · 5 hydrogen bonds · protein-protein
A–H · 346 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 27 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6ATT · 39S Fab bound to HER2 ecd · the same entry in another collection · chain A against A, TM-score 1.00
P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P04626
Elsewhere: RCSB PDB 6ATT · PDBe 6ATT · UniProt P04626

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.